Required Packages and functions

# libraries
library(sas7bdat)
library(sva)
library(reshape)
library(ggplot2)
library(gridExtra)
library(knitr)
library(dplyr)
library(kableExtra)
library(tidyverse)
library(minfi)
library(stringr)
library(limma)
library(IlluminaHumanMethylation450kanno.ilmn12.hg19)
library(minfi)
library(DMRcate)
library(UpSetR)
library(reshape)
library(corrplot)
library(factoextra)
library(ENmix)

# loading annotation
anno = getAnnotation(IlluminaHumanMethylation450kanno.ilmn12.hg19)
anno = data.frame(anno)

# loading functions
setwd('/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local')
source('EWAS functions.R')

Load DNAm and pheno data

load("/Users/annebozack/Box/NIEHS-R01 ONES/Methylation Data/Age7Blood_ComBat_Betas_Mvals_filteredProbes_metalAnalaysis.RData")

dim(pDatAge7Metal)
# 333 164

dim(ComBat.Mvalues.Metals)
# 394460    333

rownames(pDatAge7Metal) = pDatAge7Metal$samplename

pDatAge7Metal$age_yrs_7y_blood = pDatAge7Metal$c_age_days_7y_blood/365

EWAS

As

DMP_As = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'As_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As')

# Unadjusted, N =  333 
# Unadjusted, p<0.05:  23361 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  15951 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.9103149 
 
# Number of DMRs identified:   5 

# rm(DMP_As); gc()

DMRs

chr start end p length fdr sidak nprobe
2 113992761 113993313 0.00e+00 552 0.00e+00 0.0000000 8
3 46759437 46759698 0.00e+00 261 0.00e+00 0.0000006 7
17 1395863 1396123 0.00e+00 260 0.00e+00 0.0000023 5
1 228395755 228396009 0.00e+00 254 0.00e+00 0.0000061 4
17 75315562 75315667 2.65e-05 105 2.65e-05 0.0947026 3

No adjustment for fish consumption

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As/As_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As/As_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As/As_log2_manhattan_DMP_adj.png")

As, female

pDatAge7Metal_F = pDatAge7Metal[pDatAge7Metal$female_d == 1,]
pDatAge7Metal_F$race_child2 = as.factor(as.numeric(pDatAge7Metal_F$race_child2))

DMP_As_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'As_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_F')

# # Unadjusted, N =  158 
# Unadjusted, p<0.05:  26064 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  15824 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.9007317 

# Number of DMRs identified:   4 

# rm(DMP_As_F); gc()

DMRs

chr start end p length fdr sidak nprobe
1 11561496 11561711 0.0e+00 215 0.0e+00 0.0000021 3
7 76027000 76027101 0.0e+00 101 0.0e+00 0.0000095 3
2 113992842 113993142 0.0e+00 300 0.0e+00 0.0000303 5
2 198651075 198651347 6.4e-06 272 6.4e-06 0.0092121 3

No adjustment for fish consumption

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_F/As_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_F/As_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_F/As_log2_manhattan_DMP_adj.png")

As, male

pDatAge7Metal_M = pDatAge7Metal[pDatAge7Metal$female_d == 0,]
pDatAge7Metal_M$race_child2 = as.factor(as.numeric(pDatAge7Metal_M$race_child2))

DMP_As_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'As_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_M')

# Unadjusted, N =  175 
# Unadjusted, p<0.05:  11497 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  175 
# Adjusted, p<0.05:  14046 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.8408844 
 
# Number of DMRs identified:   6 

# rm(DMP_As_M); gc()

DMRs

chr start end p length fdr sidak nprobe
17 47091977 47092178 0.0000000 201 0.0000000 0.0000001 4
2 164204627 164205032 0.0000000 405 0.0000000 0.0000038 5
17 1395863 1396123 0.0000000 260 0.0000001 0.0000717 5
16 88706240 88706389 0.0000016 149 0.0000024 0.0042168 2
8 22735275 22735388 0.0000089 113 0.0000107 0.0305879 3
7 27183400 27183436 0.0062439 36 0.0062439 1.0000000 2

No adjustment for fish consumption

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_M/As_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_M/As_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_M/As_log2_manhattan_DMP_adj.png")

Ba

DMP_Ba = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Ba_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba')

# Unadjusted, N =  333 
# Unadjusted, p<0.05:  11801 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  11716 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.7753982 
 
# Number of DMRs identified:   3 

# rm(DMP_Ba); gc()

DMRs

chr start end p length fdr sidak nprobe
17 6899084 6899577 0.0000000 493 0.0000000 0.00e+00 10
16 1583809 1584118 0.0000000 309 0.0000000 2.64e-05 6
6 32145616 32145626 0.0436714 10 0.0436714 1.00e+00 2
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba/Ba_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba/Ba_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba/Ba_log2_manhattan_DMP_adj.png")

Ba, female

DMP_Ba_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Ba_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_F')

# Unadjusted, N =  158 
# Unadjusted, p<0.05:  29651 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  24029 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.224716 
 
# Number of DMRs identified:   5 

# rm(DMP_Ba_F); gc()

DMRs

chr start end p length fdr sidak nprobe
17 6899084 6899577 0.0000000 493 0.0000000 0.0000000 10
2 183943387 183943551 0.0000000 164 0.0000000 0.0000270 5
17 37123637 37123949 0.0000000 312 0.0000000 0.0000168 9
7 94285269 94285352 0.0000006 83 0.0000008 0.0029480 7
11 111250128 111250201 0.0009145 73 0.0009145 0.9928711 3
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_F/Ba_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_F/Ba_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_F/Ba_log2_manhattan_DMP_adj.png")

Ba, male

DMP_Ba_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Ba_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_M')

# Unadjusted, N =  175 
# Unadjusted, p<0.05:  25363 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  175 
# Adjusted, p<0.05:  26609 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.225518 
 
# Number of DMRs identified:   3 

rm(DMP_Ba_M); gc()

DMRs

chr start end p length fdr sidak nprobe
16 1583809 1584118 0e+00 309 0e+00 0.0000000 6
19 50194119 50194252 0e+00 133 0e+00 0.0000052 5
6 29595001 29595335 1e-07 334 1e-07 0.0001322 8
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_M/Ba_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_M/Ba_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_M/Ba_log2_manhattan_DMP_adj.png")

Cd

DMP_Cd = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Cd_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd')

# Unadjusted, N =  333 
# Unadjusted, p<0.05:  9428 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  11856 
# Adjusted, FDR<0.05:  1 
# Adjusted, pBonf<0.05:  1 
# Adjusted, lambda:  0.8163213 
 
# Number of DMRs identified:   4 

# rm(DMP_Cd); gc()

FDR-significant DMPs

cpg logFC CI.L CI.R AveExpr t P.Value adj.P.Val B adj.P.Val.bonf std_err chr pos gene end
112561 cg07044523 0.2554657 0.1719724 0.3389591 5.275559 6.019999 0 0.0019081 10.31706 0.0019081 0.042597 chr1 153514376 S100A5 153514376

DMRs

chr start end p length fdr sidak nprobe
7 158045979 158046166 0.0000000 187 0.0000000 0.0000093 3
5 23507449 23507656 0.0000000 207 0.0000000 0.0000228 5
17 46685291 46685448 0.0000000 157 0.0000001 0.0001083 5
7 27184158 27184188 0.0027811 30 0.0027811 1.0000000 4
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd/Cd_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd/Cd_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd/Cd_log2_manhattan_DMP_adj.png")

Cd, female

DMP_Cd_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Cd_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_F')

# Unadjusted, N =  158 
# Unadjusted, p<0.05:  13276 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  13473 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.8343739 
 
# Number of DMRs identified:   7 

# rm(DMP_Cd_F); gc()

DMRs

chr start end p length fdr sidak nprobe
6 32164926 32165321 0.0000000 395 0.0000000 0.0000000 7
17 46685291 46685448 0.0000000 157 0.0000000 0.0000007 5
1 26233403 26233623 0.0000000 220 0.0000001 0.0000554 8
6 1624385 1624442 0.0000001 57 0.0000001 0.0004341 2
5 23507449 23507656 0.0000001 207 0.0000001 0.0001299 5
11 73357094 73357276 0.0000022 182 0.0000025 0.0046583 6
5 132113754 132113860 0.0159548 106 0.0159548 1.0000000 3
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_F/Cd_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_F/Cd_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_F/Cd_log2_manhattan_DMP_adj.png")

Cd, male

DMP_Cd_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Cd_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_M')

# Unadjusted, N =  175 
# Unadjusted, p<0.05:  16666 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  175 
# Adjusted, p<0.05:  19722 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.070021 

# Number of DMRs identified:   3 

# rm(DMP_Cd_M); gc()

DMRs

chr start end p length fdr sidak nprobe
20 61446961 61447369 0.00e+00 408 0.00e+00 0.0000000 11
7 50518572 50518647 1.70e-06 75 2.60e-06 0.0090132 2
6 28446839 28447087 5.55e-05 248 5.55e-05 0.0844649 2
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_M/Cd_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_M/Cd_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_M/Cd_log2_manhattan_DMP_adj.png")

Cr

DMP_Cr = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Cr_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr')

# Unadjusted, N =  333 
# Unadjusted, p<0.05:  29723 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  23497 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.107048 
 
# Number of DMRs identified:   5 

# rm(DMP_Cr); gc()

DMRs

chr start end p length fdr sidak nprobe
5 145758709 145758881 0.00e+00 172 1.00e-07 0.0000526 4
16 66969473 66969500 0.00e+00 27 1.00e-07 0.0003537 2
6 33245769 33245895 8.00e-07 126 1.40e-06 0.0025854 6
19 50666378 50666538 1.65e-05 160 2.07e-05 0.0399617 3
6 33280198 33280228 2.17e-05 30 2.17e-05 0.2481969 3

No adjustment for fish consumption

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr/Cr_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr/Cr_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr/Cr_log2_manhattan_DMP_adj.png")

Cr, female

DMP_Cr_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Cr_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_F')

# Unadjusted, N =  158 
# Unadjusted, p<0.05:  26701 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  25525 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.205679 
 
# Number of identified DMR:  0

# rm(DMP_Cr_F); gc()
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_F/Cr_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_F/Cr_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_F/Cr_log2_manhattan_DMP_adj.png")

Cr, male

DMP_Cr_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Cr_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_M')

# Unadjusted, N =  175 
# Unadjusted, p<0.05:  17887 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  175 
# Adjusted, p<0.05:  12255 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.8668368 
 
# Number of DMRs identified:   1 

# rm(DMP_Cr_M); gc()

DMRs

chr start end p length fdr sidak nprobe
17 46685291 46685448 0 157 0 3.4e-06 5
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_M/Cr_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_M/Cr_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_M/Cr_log2_manhattan_DMP_adj.png")

Cs

DMP_Cs = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Cs_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs')

# Unadjusted, N =  333 
# Unadjusted, p<0.05:  16687 
# Unadjusted, FDR<0.05:  4 
# Unadjusted, pBonf<0.05:  2 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  13041 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.8278941 
 
# Number of DMRs identified:   6 

# rm(DMP_Cs); gc()

DMRs

chr start end p length fdr sidak nprobe
6 32847584 32847845 0.0000000 261 0.0000000 0.0000152 14
6 33280051 33280228 0.0000000 177 0.0000000 0.0000334 6
13 47472049 47472429 0.0000000 380 0.0000001 0.0000285 12
10 94820922 94821085 0.0000001 163 0.0000001 0.0002097 6
1 68512776 68512928 0.0000636 152 0.0000763 0.1521621 4
20 57427641 57427762 0.0010790 121 0.0010790 0.9703825 6
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs/Cs_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs/Cs_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs/Cs_log2_manhattan_DMP_adj.png")

Cs, female

DMP_Cs_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Cs_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_F')

# # Unadjusted, N =  158 
# Unadjusted, p<0.05:  25871 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  16221 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.9629794 
 
# Number of DMRs identified:   3 

# rm(DMP_Cs_F); gc()

DMRs

chr start end p length fdr sidak nprobe
1 200272111 200272215 0 104 0 7.60e-06 3
20 3145355 3145597 0 242 0 1.60e-05 3
6 29648378 29648628 0 250 0 1.97e-05 8
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_F/Cs_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_F/Cs_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_F/Cs_log2_manhattan_DMP_adj.png")

Cs, male

DMP_Cs_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Cs_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_M')

# Unadjusted, N =  175 
# Unadjusted, p<0.05:  15896 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  175 
# Adjusted, p<0.05:  13428 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.853948 
 
# Number of DMRs identified:   2 
 
# rm(DMP_Cs_M); gc()

DMRs

chr start end p length fdr sidak nprobe
20 57427442 57427942 0.0000000 500 0.0000000 0.0000005 16
1 68512776 68512845 0.0026516 69 0.0026516 0.9999997 3
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_M/Cs_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_M/Cs_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_M/Cs_log2_manhattan_DMP_adj.png")

Cu

DMP_Cu = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Cu_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu')

# Unadjusted, N =  333 
# Unadjusted, p<0.05:  10199 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  19996 
# Adjusted, FDR<0.05:  29 
# Adjusted, pBonf<0.05:  9 
# Adjusted, lambda:  1.081714 
 
# Number of DMRs identified:   18 

# rm(DMP_Cu); gc()

FDR-significant DMPs

cpg logFC CI.L CI.R AveExpr t P.Value adj.P.Val B adj.P.Val.bonf std_err chr pos gene end
1551 cg00082497 -0.2520409 -0.3556952 -0.1483866 -5.3168403 -4.784067 2.6e-06 0.0359038 2.498822 1.0000000 0.0525407 chr1 32802133 MARCKSL1 32802133
2216 cg00116766 0.4187686 0.2817760 0.5557613 2.0369340 6.014386 0.0e+00 0.0013375 6.661993 0.0019672 0.0696696 chr16 9857614 GRIN2A;GRIN2A;GRIN2A 9857614
15593 cg00908120 0.5161498 0.3285615 0.7037382 6.2592960 5.413594 1.0e-07 0.0053672 4.536415 0.0483052 0.0955715 chr16 72872925 ZFHX3;ZFHX3 72872925
36122 cg02155957 0.3783738 0.2317081 0.5250394 3.2458879 5.075841 7.0e-07 0.0144647 3.418015 0.2603651 0.0746248 chr1 46930731 46930731
66105 cg04015129 0.6991493 0.4380113 0.9602872 4.2830360 5.267633 3.0e-07 0.0077753 4.046096 0.1010794 0.1331776 chr10 1058036 GTPBP4 1058036
76780 cg04692924 -0.4221533 -0.5884130 -0.2558937 -6.6080183 -4.995731 1.0e-06 0.0182608 3.161088 0.3834770 0.0846568 chr1 161720042 DUSP12 161720042
82479 cg05051957 -0.4539930 -0.6266037 -0.2813824 -5.5960973 -5.174845 4.0e-07 0.0103119 3.739885 0.1603134 0.0879075 chr8 141522459 CHRAC1;CHRAC1 141522459
96056 cg05955013 -0.3954311 -0.5455648 -0.2452975 -6.2800794 -5.182132 4.0e-07 0.0103119 3.763782 0.1546451 0.0763997 chr17 45056646 RPRML 45056646
107200 cg06723863 -0.2584074 -0.3627173 -0.1540976 -5.9821329 -4.874088 1.7e-06 0.0262890 2.777821 0.6835148 0.0528782 chr16 68270129 ESRP2;ESRP2 68270129
117957 cg07380021 -0.5074974 -0.6911466 -0.3238481 -5.4168894 -5.437012 1.0e-07 0.0053558 4.616053 0.0428465 0.0935562 chr1 206755252 RASSF5;RASSF5;RASSF5 206755252
124637 cg07831553 0.6064739 0.3579392 0.8550087 3.3703905 4.801100 2.4e-06 0.0343734 2.550888 0.9624563 0.1267359 chr19 48796974 48796974
132730 cg08370347 0.5104082 0.3050049 0.7158114 3.9077562 4.889066 1.6e-06 0.0254900 2.824231 0.6372491 0.1046840 chr5 171571793 STK10 171571793
157990 cg10145926 0.6116469 0.3869329 0.8363609 5.3066802 5.355331 2.0e-07 0.0059077 4.339440 0.0649842 0.1145586 chr14 95875792 C14orf139 95875792
165306 cg10653573 0.8216430 0.4935682 1.1497177 5.4323036 4.927492 1.3e-06 0.0241467 2.944904 0.5312281 0.1673806 chr8 141347297 TRAPPC9;TRAPPC9 141347297
168880 cg10923018 0.2400925 0.1567575 0.3234276 2.7547510 5.668452 0.0e+00 0.0025621 5.418042 0.0128106 0.0420591 chr6 31743769 C6orf27 31743769
178008 cg11608893 0.6111347 0.3655771 0.8566923 6.0473017 4.896652 1.6e-06 0.0254900 2.847992 0.6148187 0.1252142 chr6 32059542 TNXB 32059542
184513 cg12067421 -0.4638647 -0.6195019 -0.3082274 2.0086375 -5.863991 0.0e+00 0.0014972 6.113861 0.0044916 0.0792183 chr1 203246482 203246482
202444 cg13434714 -0.4198573 -0.5838480 -0.2558666 -5.7702697 -5.037302 8.0e-07 0.0165199 3.293966 0.3138780 0.0834953 chr12 6936787 LEPREL2 6936787
238372 cg15790767 1.0460317 0.6730623 1.4190011 3.8395189 5.518071 1.0e-07 0.0040292 4.893762 0.0282044 0.1903147 chr6 13431216 GFOD1 13431216
257054 cg17143270 0.8262133 0.5117283 1.1406983 5.7439128 5.169016 4.0e-07 0.0103119 3.720792 0.1649911 0.1604376 chr1 91532819 91532819
272331 cg18299835 -0.2325838 -0.3271320 -0.1380356 -4.1342108 -4.839937 2.0e-06 0.0297198 2.671477 0.8024340 0.0478488 chr19 13207445 NFIX 13207445
277756 cg18714712 -0.5396013 -0.7177693 -0.3614334 -5.9732941 -5.958802 0.0e+00 0.0013375 6.457915 0.0026750 0.0907515 chr19 49866917 DKKL1;TEAD2 49866917
288096 cg19532212 0.4901147 0.3073681 0.6728612 4.4622674 5.276722 2.0e-07 0.0077753 4.076321 0.0965815 0.0930943 chr17 56769430 TEX14;RAD51C;TEX14;RAD51C 56769430
292461 cg19842134 -0.2877291 -0.4005045 -0.1749537 -3.5252232 -5.019759 9.0e-07 0.0170704 3.238255 0.3414082 0.0572337 chr12 54070591 ATP5G2;ATP5G2 54070591
299106 cg20365618 -0.2427541 -0.3400297 -0.1454786 0.4203879 -4.909944 1.5e-06 0.0250879 2.890132 0.5770213 0.0492549 chr10 121578384 INPP5F;INPP5F 121578384
338217 cg23477849 0.2847709 0.1875717 0.3819701 4.8779575 5.764299 0.0e+00 0.0019215 5.757320 0.0076859 0.0492155 chr19 5698492 LONP1 5698492
370410 cg25954729 -0.2214209 -0.3023661 -0.1404758 -6.3449744 -5.381973 1.0e-07 0.0056715 4.429925 0.0567155 0.0408229 chr11 66610784 RCE1;C11orf80;RCE1 66610784
381104 cg26708724 0.6610798 0.4075131 0.9146465 6.7325633 5.129526 5.0e-07 0.0117853 3.591901 0.2003502 0.1293079 chr4 187509785 FAT1 187509785
393045 cg27565067 0.4808885 0.3122348 0.6495422 6.2036309 5.610017 0.0e+00 0.0029086 5.212584 0.0174516 0.0858822 chr17 149484 RPH3AL 149484

DMRs

chr start end p length fdr sidak nprobe
22 45704901 45705265 0.0e+00 364 0.0e+00 0.0000000 7
20 35169538 35169886 0.0e+00 348 0.0e+00 0.0000000 6
16 66304366 66304585 0.0e+00 219 0.0e+00 0.0000001 3
10 121578136 121578639 0.0e+00 503 0.0e+00 0.0000001 4
12 54070516 54070610 0.0e+00 94 0.0e+00 0.0000006 5
16 8806530 8806756 0.0e+00 226 0.0e+00 0.0000005 7
17 149483 149488 0.0e+00 5 0.0e+00 0.0001478 2
6 1604012 1604212 0.0e+00 200 0.0e+00 0.0000156 5
20 3052114 3052483 0.0e+00 369 0.0e+00 0.0000175 9
17 1395863 1396123 0.0e+00 260 0.0e+00 0.0000380 5
19 55660590 55660625 0.0e+00 35 0.0e+00 0.0002927 4
15 100048370 100048500 0.0e+00 130 0.0e+00 0.0000987 3
2 130345204 130345405 0.0e+00 201 1.0e-07 0.0000951 3
17 47091977 47092178 1.0e-07 201 1.0e-07 0.0001346 4
19 50194119 50194252 1.0e-07 133 1.0e-07 0.0002220 5
13 100310161 100310405 1.0e-07 244 1.0e-07 0.0001692 4
11 19736149 19736333 1.0e-07 184 1.0e-07 0.0002958 5
1 207082827 207082900 1.1e-06 73 1.1e-06 0.0057588 2
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu/Cu_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu/Cu_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu/Cu_log2_manhattan_DMP_adj.png")

Cu, female

DMP_Cu_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Cu_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_F')

# Unadjusted, N =  158 
# Unadjusted, p<0.05:  19233 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  16206 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.9568499 
 
# Number of DMRs identified:   11 

# rm(DMP_Cu_F); gc()

DMRs

chr start end p length fdr sidak nprobe
5 191295 191806 0.0000000 511 0.0000000 0.0000000 9
6 32063990 32064810 0.0000000 820 0.0000000 0.0000000 30
15 81426346 81426610 0.0000000 264 0.0000000 0.0000002 7
11 73357094 73357396 0.0000000 302 0.0000001 0.0000436 7
2 74875226 74875536 0.0000001 310 0.0000001 0.0000721 7
1 120174148 120174361 0.0000001 213 0.0000002 0.0002162 2
17 1395863 1396123 0.0000001 260 0.0000002 0.0002000 5
21 37442288 37442476 0.0000001 188 0.0000002 0.0002909 3
8 95962351 95962383 0.0000021 32 0.0000025 0.0252792 4
19 23941312 23941438 0.0001150 126 0.0001265 0.3023269 3
6 31734291 31734401 0.0008058 110 0.0008058 0.9444595 3
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_F/Cu_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_F/Cu_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_F/Cu_log2_manhattan_DMP_adj.png")

Cu, male

DMP_Cu_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Cu_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_M')

# Unadjusted, N =  175 
# Unadjusted, p<0.05:  8255 
# Unadjusted, FDR<0.05:  32 
# Unadjusted, pBonf<0.05:  5 
 
# Adjusted, N =  175 
# Adjusted, p<0.05:  11955 
# Adjusted, FDR<0.05:  43 
# Adjusted, pBonf<0.05:  13 
# Adjusted, lambda:  0.732688 
 
# Number of DMRs identified:   13 

# rm(DMP_Cu_M); gc()

FDR-significant DMPs

cpg logFC CI.L CI.R AveExpr t P.Value adj.P.Val B adj.P.Val.bonf std_err chr pos gene end
15593 cg00908120 0.6968301 0.4462335 0.9474266 6.2892750 5.491907 2.0e-07 0.0043618 3.025092 0.0610657 0.1275144 chr16 72872925 ZFHX3;ZFHX3 72872925
17338 cg01007589 0.9199500 0.5976038 1.2422962 4.7896683 5.636547 1.0e-07 0.0027740 3.404180 0.0305142 0.1642702 chr19 49894178 CCDC155 49894178
18335 cg01063965 -0.2697333 -0.3700510 -0.1694156 -6.4353826 -5.310319 4.0e-07 0.0095478 2.558610 0.1432177 0.0499143 chr11 695461 TMEM80;TMEM80;DEAF1;DEAF1 695461
24635 cg01447660 0.3857890 0.2320438 0.5395341 -0.9207246 4.955781 1.8e-06 0.0211997 1.670256 0.7207908 0.0777249 chr2 69152678 69152678
25210 cg01485439 0.5040485 0.3119450 0.6961521 3.6452587 5.182127 7.0e-07 0.0123633 2.231633 0.2596284 0.0974910 chr11 67225937 CABP4 67225937
36122 cg02155957 0.4849601 0.2932852 0.6766350 3.2214886 4.997028 1.5e-06 0.0198854 1.770337 0.6006643 0.0972710 chr1 46930731 46930731
41497 cg02490920 0.3674539 0.2288810 0.5060267 1.3358885 5.237070 5.0e-07 0.0105880 2.372126 0.2011721 0.0698665 chr3 50304406 SEMA3B;SEMA3B 50304406
49479 cg02968175 0.3051401 0.1909359 0.4193442 5.7555141 5.276926 4.0e-07 0.0098398 2.473410 0.1672768 0.0571880 chr16 4690020 MGRN1;MGRN1;MGRN1;MGRN1 4690020
61452 cg03717239 0.2988200 0.1782864 0.4193536 0.5057733 4.896268 2.4e-06 0.0247759 1.524790 0.9385842 0.0604897 chr8 145574318 145574318
66105 cg04015129 0.8389384 0.5547224 1.1231543 4.2710633 5.829792 0.0e+00 0.0013191 3.918551 0.0118723 0.1447437 chr10 1058036 GTPBP4 1058036
72385 cg04406071 -0.2980754 -0.4100451 -0.1861057 -6.0707229 -5.257620 5.0e-07 0.0101631 2.424293 0.1829363 0.0560206 chr17 59489784 C17orf82 59489784
76780 cg04692924 -0.5914287 -0.8226470 -0.3602104 -6.5844679 -5.051864 1.2e-06 0.0187815 1.905864 0.4695367 0.1175757 chr1 161720042 DUSP12 161720042
82479 cg05051957 -0.6067193 -0.8484554 -0.3649831 -5.6069817 -4.956986 1.8e-06 0.0211997 1.671792 0.7183584 0.1229709 chr8 141522459 CHRAC1;CHRAC1 141522459
96056 cg05955013 -0.4736694 -0.6647461 -0.2825927 -6.2968923 -4.895966 2.4e-06 0.0247759 1.522807 0.9414854 0.0969641 chr17 45056646 RPRML 45056646
117957 cg07380021 -0.6727208 -0.8917216 -0.4537201 -5.4253082 -6.066814 0.0e+00 0.0010386 4.560897 0.0036354 0.1113060 chr1 206755252 RASSF5;RASSF5;RASSF5 206755252
132177 cg08329655 -0.4301609 -0.5996488 -0.2606731 -5.8759956 -5.012548 1.4e-06 0.0198854 1.809564 0.5595710 0.0858576 chr11 7534677 PPFIBP2 7534677
133940 cg08459368 0.5800924 0.3505524 0.8096324 2.7047867 4.991261 1.6e-06 0.0198854 1.756039 0.6164462 0.1167147 chr11 61974948 SCGB2A1 61974948
138326 cg08760128 0.3023438 0.1838403 0.4208473 6.7313293 5.038874 1.3e-06 0.0191075 1.875166 0.4967943 0.0594315 chr16 4723507 MGRN1;MGRN1;MGRN1;MGRN1 4723507
159790 cg10266648 1.0455372 0.6777917 1.4132828 5.9758418 5.615177 1.0e-07 0.0028193 3.347846 0.0338314 0.1875055 chr2 106560529 106560529
168880 cg10923018 0.3493522 0.2386925 0.4600120 2.7253233 6.235017 0.0e+00 0.0007687 5.027037 0.0015374 0.0553357 chr6 31743769 C6orf27 31743769
178008 cg11608893 0.9384948 0.6293671 1.2476226 6.0805801 5.996051 0.0e+00 0.0010386 4.367865 0.0051911 0.1575025 chr6 32059542 TNXB 32059542
202444 cg13434714 -0.6677598 -0.8632470 -0.4722727 -5.7834106 -6.746422 0.0e+00 0.0001057 6.462646 0.0001057 0.0992288 chr12 6936787 LEPREL2 6936787
211983 cg13989834 0.5445790 0.3327048 0.7564532 3.1425732 5.076382 1.1e-06 0.0175131 1.966788 0.4203137 0.1076471 chr9 134400392 UCK1;UCK1 134400392
232975 cg15389183 -0.2174854 -0.3060013 -0.1289694 -6.1941560 -4.852574 2.9e-06 0.0291746 1.418688 1.0000000 0.0436880 chr14 102829482 TECPR2;CINP 102829482
238372 cg15790767 1.1582593 0.6788697 1.6376489 3.8648959 4.771870 4.1e-06 0.0386055 1.223075 1.0000000 0.2446072 chr6 13431216 GFOD1 13431216
242146 cg16068812 -1.0140695 -1.4211959 -0.6069431 -4.2669662 -4.919374 2.2e-06 0.0241887 1.579759 0.8489923 0.2076521 chr21 44528396 U2AF1;U2AF1;U2AF1 44528396
248112 cg16496814 0.2786227 0.1688097 0.3884356 5.2206210 5.011024 1.4e-06 0.0198854 1.806255 0.5630518 0.0548928 chr11 9778721 9778721
250632 cg16656826 0.3287551 0.2038843 0.4536259 0.1436170 5.199664 6.0e-07 0.0119506 2.277470 0.2390116 0.0627483 chr5 159343871 ADRA1B;ADRA1B 159343871
277216 cg18670846 0.7273051 0.4270507 1.0275594 -2.3046149 4.784083 3.9e-06 0.0382303 1.252345 1.0000000 0.1529585 chr2 68917482 68917482
277756 cg18714712 -0.7278273 -0.9713903 -0.4842644 -5.9498636 -5.901856 0.0e+00 0.0010386 4.112559 0.0083088 0.1239078 chr19 49866917 DKKL1;TEAD2 49866917
281545 cg19005275 0.6770397 0.4430316 0.9110478 4.2897154 5.714189 1.0e-07 0.0020931 3.609791 0.0209309 0.1190070 chr12 113588263 CCDC42B 113588263
288096 cg19532212 0.6853542 0.4290550 0.9416534 4.4209486 5.281281 4.0e-07 0.0098398 2.482710 0.1643357 0.1304380 chr17 56769430 TEX14;RAD51C;TEX14;RAD51C 56769430
299106 cg20365618 -0.3482548 -0.4639507 -0.2325589 0.4046566 -5.944876 0.0e+00 0.0010386 4.231669 0.0066813 0.0579668 chr10 121578384 INPP5F;INPP5F 121578384
301945 cg20597842 0.9761061 0.5701079 1.3821044 5.8802068 4.748367 4.6e-06 0.0417512 1.166880 1.0000000 0.2070751 chr12 7818585 APOBEC1 7818585
311691 cg21373263 0.7831825 0.4817236 1.0846414 3.2926911 5.131051 8.0e-07 0.0149060 2.103265 0.3279323 0.1535754 chr10 126751982 CTBP2;CTBP2 126751982
317735 cg21864868 0.6556443 0.4008014 0.9104871 4.2151756 5.081211 1.0e-06 0.0175131 1.978806 0.4112293 0.1296914 chr17 46673002 LOC404266;LOC404266;LOC404266;LOC404266;LOC404266 46673002
322216 cg22240394 1.0541992 0.6343256 1.4740728 6.8239404 4.958788 1.8e-06 0.0211997 1.676215 0.7126127 0.2141721 chr3 186211630 186211630
322745 cg22286640 -0.7778819 -1.0993127 -0.4564511 -4.6467158 -4.779666 4.0e-06 0.0382303 1.241753 1.0000000 0.1638016 chr8 67026828 67026828
336099 cg23312431 0.3344962 0.2000374 0.4689549 -0.3693187 4.913215 2.2e-06 0.0241887 1.566102 0.8707948 0.0677317 chr21 45773997 TRPM2 45773997
338217 cg23477849 0.3799812 0.2454369 0.5145256 4.8962493 5.577768 1.0e-07 0.0031066 3.251684 0.0403856 0.0677761 chr19 5698492 LONP1 5698492
352329 cg24543538 0.8446393 0.5105801 1.1786986 3.2168166 4.993663 1.5e-06 0.0198854 1.761957 0.6098552 0.1702661 chr2 241569846 GPR35 241569846
370410 cg25954729 -0.3031186 -0.4042129 -0.2020244 -6.3724574 -5.921746 0.0e+00 0.0010386 4.169016 0.0074984 0.0503223 chr11 66610784 RCE1;C11orf80;RCE1 66610784
381104 cg26708724 0.9627258 0.6436003 1.2818513 6.7173655 5.958165 0.0e+00 0.0010386 4.264949 0.0062755 0.1626214 chr4 187509785 FAT1 187509785

DMRs

chr start end p length fdr sidak nprobe
10 121578136 121578846 0.0000000 710 0.0000000 0.0000000 5
22 45704901 45705265 0.0000000 364 0.0000000 0.0000000 7
21 45773781 45773997 0.0000000 216 0.0000000 0.0000015 2
4 24796918 24797176 0.0000000 258 0.0000000 0.0000032 6
19 50194119 50194252 0.0000000 133 0.0000000 0.0000267 5
17 70723226 70723386 0.0000000 160 0.0000000 0.0000317 2
20 35169593 35169886 0.0000000 293 0.0000001 0.0000422 5
14 78447480 78447640 0.0000001 160 0.0000001 0.0001307 3
3 16216093 16216215 0.0000001 122 0.0000001 0.0001905 4
17 78549323 78549371 0.0000001 48 0.0000001 0.0006222 3
17 149483 149488 0.0000001 5 0.0000001 0.0080723 2
12 54070516 54070591 0.0000149 75 0.0000161 0.0752227 4
16 8806752 8806756 0.0029944 4 0.0029944 1.0000000 2
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_M/Cu_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_M/Cu_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_M/Cu_log2_manhattan_DMP_adj.png")

Hg

DMP_Hg = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Hg_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg')

# Unadjusted, N =  326 
# Unadjusted, p<0.05:  37293 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  326 
# Adjusted, p<0.05:  27145 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.2206 
 
# Number of DMRs identified:   4 

# rm(DMP_Hg); gc()

DMRs

chr start end p length fdr sidak nprobe
17 46681110 46681401 0.0000000 291 0.0000000 0.0000007 6
6 31846768 31847009 0.0000000 241 0.0000000 0.0000093 9
10 131843516 131843725 0.0000022 209 0.0000030 0.0042060 3
3 42977952 42978026 0.0004262 74 0.0004262 0.8969299 2
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg/Hg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg/Hg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg/Hg_log2_manhattan_DMP_adj.png")

Hg, female

DMP_Hg_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Hg_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_F')

# Unadjusted, N =  154 
# Unadjusted, p<0.05:  35686 
# Unadjusted, FDR<0.05:  156 
# Unadjusted, pBonf<0.05:  1 
 
# Adjusted, N =  154 
# Adjusted, p<0.05:  15067 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.8813254 
 
# Number of DMRs identified:   3 

# rm(DMP_Hg_F); gc()

DMRs

chr start end p length fdr sidak nprobe
12 47219625 47220092 0 467 0 0.00e+00 12
4 165877874 165878136 0 262 0 2.10e-06 6
7 27143234 27143478 0 244 0 2.93e-05 7
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_F/Hg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_F/Hg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_F/Hg_log2_manhattan_DMP_adj.png")

Hg, male

DMP_Hg_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Hg_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_M')

# Unadjusted, N =  172 
# Unadjusted, p<0.05:  22412 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  172 
# Adjusted, p<0.05:  24779 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.2248 
 
# Number of DMRs identified:   7 

# rm(DMP_Hg_M); gc()

DMRs

chr start end p length fdr sidak nprobe
6 31846768 31847009 0e+00 241 0e+00 0.0000000 9
11 18477152 18477534 0e+00 382 0e+00 0.0000001 7
11 18433499 18433887 0e+00 388 0e+00 0.0000001 5
5 502290 502571 0e+00 281 0e+00 0.0000015 3
6 33282735 33283162 0e+00 427 0e+00 0.0000011 20
14 104690039 104690244 0e+00 205 0e+00 0.0000132 5
1 2345151 2345410 1e-07 259 1e-07 0.0001903 8
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_M/Hg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_M/Hg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_M/Hg_log2_manhattan_DMP_adj.png")

Mg

DMP_Mg = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Mg_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg')

# Unadjusted, N =  333 
# Unadjusted, p<0.05:  18232 
# Unadjusted, FDR<0.05:  1 
# Unadjusted, pBonf<0.05:  1 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  15989 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.8804657 
 
# Number of DMRs identified:   4 

# rm(DMP_Mg); gc()

DMRs

chr start end p length fdr sidak nprobe
20 3051953 3052345 0.0e+00 392 0.0e+00 0.0000000 9
6 31543539 31543686 0.0e+00 147 0.0e+00 0.0000326 8
2 240196768 240196996 0.0e+00 228 1.0e-07 0.0000792 3
11 368564 368712 1.9e-06 148 1.9e-06 0.0049840 7
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg/Mg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg/Mg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg/Mg_log2_manhattan_DMP_adj.png")

Mg, female

DMP_Mg_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Mg_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_F')

# Unadjusted, N =  158 
# Unadjusted, p<0.05:  33977 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  20666 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.081664 
 
# Number of DMRs identified:   2 

# rm(DMP_Mg_F); gc()

DMRs

chr start end p length fdr sidak nprobe
2 240196876 240196996 0.0000008 120 0.0000016 0.0025678 2
6 10884093 10884140 0.0002591 47 0.0002591 0.8863834 2
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_F/Mg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_F/Mg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_F/Mg_log2_manhattan_DMP_adj.png")

Mg, male

DMP_Mg_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Mg_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_M')

# Unadjusted, N =  175 
# Unadjusted, p<0.05:  9395 
# Unadjusted, FDR<0.05:  7 
# Unadjusted, pBonf<0.05:  5 
 
# Adjusted, N =  175 
# Adjusted, p<0.05:  13518 
# Adjusted, FDR<0.05:  3 
# Adjusted, pBonf<0.05:  3 
# Adjusted, lambda:  0.8045591 

# Number of identified DMR:  0

# rm(DMP_Mg_M); gc()

FDR-significant DMPs

DMRs

chr start end p length fdr sidak nprobe
21 45773781 45773997 0.0000000 216 0.0000000 0.0000013 2
17 37123637 37123949 0.0000000 312 0.0000001 0.0000317 9
5 23507449 23507656 0.0000000 207 0.0000002 0.0000915 5
2 152830504 152830665 0.0000001 161 0.0000003 0.0002264 5
17 47091977 47092178 0.0000001 201 0.0000003 0.0002324 4
10 121578383 121578639 0.0000003 256 0.0000005 0.0003992 3
6 31543539 31543686 0.0000004 147 0.0000006 0.0010323 8
3 138725152 138725425 0.0000004 273 0.0000006 0.0006235 7
12 54385274 54385526 0.0000008 252 0.0000009 0.0012112 4
17 70723226 70723386 0.0000013 160 0.0000014 0.0032358 2
11 368564 368638 0.0002279 74 0.0002279 0.7033206 5
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_M/Mg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_M/Mg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_M/Mg_log2_manhattan_DMP_adj.png")

Mn

DMP_Mn = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Mn_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn')

# Unadjusted, N =  333 
# Unadjusted, p<0.05:  27983 
# Unadjusted, FDR<0.05:  6 
# Unadjusted, pBonf<0.05:  1 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  39149 
# Adjusted, FDR<0.05:  14 
# Adjusted, pBonf<0.05:  3 
# Adjusted, lambda:  1.35996 
 
# Number of DMRs identified:   7 

# rm(DMP_Mn); gc()

FDR-significant DMPs

cpg logFC CI.L CI.R AveExpr t P.Value adj.P.Val B adj.P.Val.bonf std_err chr pos gene end
13985 cg00808511 0.1797749 0.1076657 0.2518840 2.8599969 4.905172 1.5e-06 0.0441677 4.921202 0.5905329 0.0367425 chr16 52495237 TOX3;TOX3 52495237
61437 cg03716590 0.1820431 0.1108155 0.2532707 5.0904967 5.028534 8.0e-07 0.0327455 5.457274 0.3274551 0.0362916 chr7 95435309 DYNC1I1;DYNC1I1;DYNC1I1 95435309
90890 cg05613017 0.1995162 0.1227136 0.2763187 5.3286885 5.111142 6.0e-07 0.0272713 5.822518 0.2192172 0.0391431 chr12 65589446 LEMD3;LEMD3 65589446
153815 cg09856068 -0.1132155 -0.1568602 -0.0695708 -4.3655995 -5.103735 6.0e-07 0.0272713 5.790109 0.2271515 0.0221605 chr5 170878246 FGF18 170878246
170758 cg11063328 -0.1609044 -0.2222669 -0.0995418 -6.0173655 -5.159174 4.0e-07 0.0272713 6.037176 0.1731901 0.0312433 chr11 18343203 GTF2H1;HPS5;HPS5;HPS5;GTF2H1 18343203
171438 cg11115211 -0.1889357 -0.2648699 -0.1130014 -5.8811483 -4.895440 1.6e-06 0.0441677 4.879395 0.6183473 0.0386990 chr3 67704890 SUCLG2 67704890
209344 cg13834844 -0.1019035 -0.1391228 -0.0646842 -5.1364932 -5.386845 1.0e-07 0.0138315 7.077995 0.0553259 0.0188544 chr10 102415320 102415320
216559 cg14252211 0.1929530 0.1274370 0.2584689 5.8503162 5.794555 0.0e+00 0.0032695 9.031255 0.0065390 0.0333691 chr1 25919394 25919394
286458 cg19407717 0.3110043 0.2209750 0.4010336 4.0277865 6.796700 0.0e+00 0.0000211 14.301558 0.0000211 0.0459058 chr2 1544120 TPO;TPO;TPO;TPO 1544120
286677 cg19425870 -0.1477253 -0.2059407 -0.0895098 -6.4570149 -4.992663 1.0e-06 0.0353787 5.300234 0.3891653 0.0296320 chr11 3876808 STIM1 3876808
326256 cg22586726 0.2701506 0.1619704 0.3783308 -0.9735686 4.913305 1.4e-06 0.0441677 4.956198 0.5682174 0.0551823 chr10 134150542 LRRC27;LRRC27;LRRC27;LRRC27;LRRC27 134150542
347861 cg24196240 0.3273967 0.2094577 0.4453357 5.2479144 5.461758 1.0e-07 0.0125768 7.427654 0.0377305 0.0601685 chr21 36096009 NCRNA00160 36096009
359777 cg25101184 0.2474977 0.1517913 0.3432040 3.3810389 5.087987 6.0e-07 0.0272713 5.719635 0.2454421 0.0488076 chr14 56231604 RPL13AP3 56231604
386595 cg27095984 -0.1889690 -0.2595782 -0.1183597 5.2710750 -5.265561 3.0e-07 0.0204265 6.518590 0.1021325 0.0359752 chr13 21652115 21652115

DMRs

chr start end p length fdr sidak nprobe
10 134150488 134150760 0.0000000 272 0.0000000 0.0000000 7
19 21657528 21657756 0.0000000 228 0.0000000 0.0000001 4
16 30572738 30573013 0.0000000 275 0.0000000 0.0000011 5
16 73100425 73100510 0.0000000 85 0.0000000 0.0001111 2
10 45406680 45406847 0.0000000 167 0.0000000 0.0000744 3
20 61659979 61660250 0.0000001 271 0.0000001 0.0000929 2
10 35484767 35484824 0.0002039 57 0.0002039 0.7560663 3
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn/Mn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn/Mn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn/Mn_log2_manhattan_DMP_adj.png")

Mn, female

DMP_Mn_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Mn_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_F')

# Unadjusted, N =  158 
# Unadjusted, p<0.05:  28256 
# Unadjusted, FDR<0.05:  3 
# Unadjusted, pBonf<0.05:  3 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  40111 
# Adjusted, FDR<0.05:  3 
# Adjusted, pBonf<0.05:  3 
# Adjusted, lambda:  1.365691 
 
# Number of DMRs identified:   2 

# rm(DMP_Mn_F); gc()

FDR-significant DMPs

cpg logFC CI.L CI.R AveExpr t P.Value adj.P.Val B adj.P.Val.bonf std_err chr pos gene end
170758 cg11063328 -0.2542536 -0.3311487 -0.1773585 -6.003312 -6.536372 0e+00 0.0004165 11.101209 0.0004165 0.0390272 chr11 18343203 GTF2H1;HPS5;HPS5;HPS5;GTF2H1 18343203
286677 cg19425870 -0.2408160 -0.3166778 -0.1649541 -6.446281 -6.275239 0e+00 0.0007852 9.941850 0.0015705 0.0384954 chr11 3876808 STIM1 3876808
324070 cg22396353 -0.1482285 -0.2007424 -0.0957146 -6.101068 -5.579761 1e-07 0.0154847 6.983409 0.0464542 0.0264223 chr22 46692687 GTSE1;GTSE1;CN5H6.4 46692687

DMRs

chr start end p length fdr sidak nprobe
6 3849380 3849702 0.0e+00 322 1.0e-07 0.0000351 13
11 76839190 76839217 5.3e-06 27 5.3e-06 0.0742406 3
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_F/Mn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_F/Mn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_F/Mn_log2_manhattan_DMP_adj.png")

Mn, male

DMP_Mn_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Mn_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_M')

Unadjusted, N =  175 
Unadjusted, p<0.05:  14905 
Unadjusted, FDR<0.05:  27 
Unadjusted, pBonf<0.05:  9 
 
Adjusted, N =  175 
Adjusted, p<0.05:  19138 
Adjusted, FDR<0.05:  30 
Adjusted, pBonf<0.05:  13 
Adjusted, lambda:  0.9881206 
 
Number of DMRs identified:   12 

# rm(DMP_Mn_M); gc()
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_M/Mn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_M/Mn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_M/Mn_log2_manhattan_DMP_adj.png")

FDR-significant DMPs

cpg logFC CI.L CI.R AveExpr t P.Value adj.P.Val B adj.P.Val.bonf std_err chr pos gene end
56695 cg03425412 -0.2215880 -0.3084393 -0.1347367 -5.940582 -5.038959 1.3e-06 0.0226177 4.630103 0.4975885 0.0440754 chr20 21500337 21500337
68153 cg04143120 0.4096425 0.2732188 0.5460663 6.792018 5.930435 0.0e+00 0.0010296 8.159475 0.0072071 0.0694995 chr11 72968848 72968848
79809 cg04885068 0.1877474 0.1216510 0.2538439 6.474553 5.609957 1.0e-07 0.0032325 6.851750 0.0345882 0.0333719 chr1 9099298 SLC2A5;SLC2A5 9099298
82300 cg05041382 -0.1229809 -0.1725540 -0.0734078 -6.391825 -4.899538 2.3e-06 0.0330400 4.114159 0.9251202 0.0247765 chr13 50366546 KPNA3 50366546
85445 cg05249026 -0.1644832 -0.2257280 -0.1032385 -2.355604 -5.304156 4.0e-07 0.0081883 5.643430 0.1473888 0.0308565 chr16 11031524 DEXI 11031524
97510 cg06051716 0.3566344 0.2441486 0.4691202 6.493667 6.261770 0.0e+00 0.0002468 9.558316 0.0013459 0.0572337 chr6 169225783 169225783
107728 cg06756211 -0.2081794 -0.2740447 -0.1423141 -6.049441 -6.242302 0.0e+00 0.0002468 9.478836 0.0014809 0.0332522 chr1 223936799 CAPN2;CAPN2 223936799
109948 cg06883949 -0.1214334 -0.1679112 -0.0749557 -6.468868 -5.160082 7.0e-07 0.0143290 5.089503 0.2865793 0.0231544 chr4 1795240 FGFR3;FGFR3;FGFR3 1795240
128092 cg08072480 -0.1393237 -0.1948333 -0.0838141 -6.612619 -4.957019 1.8e-06 0.0298678 4.326339 0.7168284 0.0278749 chr11 65292666 SCYL1;SCYL1 65292666
157031 cg10088075 -0.1106800 -0.1561537 -0.0652063 -6.213891 -4.806981 3.5e-06 0.0463062 3.776162 1.0000000 0.0226270 chr16 30407103 ZNF48;ZNF48 30407103
176390 cg11480534 0.3975879 0.2442723 0.5509035 5.838834 5.121748 9.0e-07 0.0162915 4.941954 0.3421211 0.0781475 chr11 62255850 AHNAK 62255850
176843 cg11521780 -0.1371987 -0.1836223 -0.0907750 -5.767858 -5.836788 0.0e+00 0.0014287 7.775114 0.0114294 0.0231260 chr12 53693949 C12orf10 53693949
180100 cg11755803 0.4054795 0.2439920 0.5669669 5.790724 4.959083 1.8e-06 0.0298678 4.332328 0.7116767 0.0823297 chr12 129000542 TMEM132C 129000542
192975 cg12700904 -0.1026171 -0.1442559 -0.0609784 -5.936497 -4.867273 2.7e-06 0.0367795 3.995819 1.0000000 0.0206063 chr3 13590720 FBLN2;FBLN2 13590720
194538 cg12828656 -0.1505408 -0.1978614 -0.1032201 -0.497092 -6.283003 0.0e+00 0.0002468 9.653365 0.0012011 0.0235966 chr5 132577108 FSTL4 132577108
209344 cg13834844 -0.1537219 -0.2150872 -0.0923565 -5.125143 -4.947389 1.9e-06 0.0299292 4.290672 0.7482293 0.0309191 chr10 102415320 102415320
209541 cg13848566 -0.1657616 -0.2254232 -0.1061000 -6.364105 -5.487225 2.0e-07 0.0041510 6.361612 0.0622649 0.0300344 chr9 89561175 GAS1 89561175
214672 cg14149680 -0.2933548 -0.3823188 -0.2043908 -6.352664 -6.512538 0.0e+00 0.0001218 10.644399 0.0003654 0.0451606 chr11 2187632 TH;TH;TH 2187632
249118 cg16560774 -0.1674158 -0.2247905 -0.1100411 -6.459545 -5.762880 0.0e+00 0.0018270 7.471818 0.0164430 0.0288456 chr17 79373381 BAHCC1 79373381
286458 cg19407717 0.4941274 0.3507014 0.6375534 4.033610 6.804284 0.0e+00 0.0000420 11.935137 0.0000775 0.0730850 chr2 1544120 TPO;TPO;TPO;TPO 1544120
287817 cg19511862 -0.1036380 -0.1427175 -0.0645584 -6.258253 -5.237605 5.0e-07 0.0105619 5.386300 0.2006761 0.0192509 chr12 125478458 BRI3BP 125478458
289598 cg19641404 -0.1138848 -0.1597132 -0.0680564 -5.865794 -4.907886 2.3e-06 0.0330400 4.144868 0.8915828 0.0228134 chr2 232826272 DIS3L2 232826272
299702 cg20414082 0.2602966 0.1634793 0.3571138 3.200594 5.309910 4.0e-07 0.0081883 5.663610 0.1438533 0.0491946 chr1 203002593 203002593
300828 cg20504533 -0.2169473 -0.2800653 -0.1538293 -5.852235 -6.788360 0.0e+00 0.0000420 11.869177 0.0000839 0.0318283 chr17 15848253 ADORA2B;ADORA2B 15848253
326031 cg22563312 -0.1654587 -0.2241965 -0.1067209 -6.274307 -5.563337 1.0e-07 0.0033295 6.664767 0.0432836 0.0295544 chr5 179334739 TBC1D9B;TBC1D9B 179334739
327739 cg22702772 -0.1485121 -0.2011945 -0.0958296 -6.685949 -5.567491 1.0e-07 0.0033295 6.681390 0.0424292 0.0264012 chr3 48699012 CELSR3 48699012
347861 cg24196240 0.4158514 0.2668619 0.5648410 5.267386 5.512565 1.0e-07 0.0039531 6.459776 0.0553431 0.0759332 chr21 36096009 NCRNA00160 36096009
357841 cg24948962 -0.2158814 -0.2919582 -0.1398046 -5.437432 -5.604397 1.0e-07 0.0032325 6.828678 0.0355576 0.0385319 chr18 2906032 EMILIN2 2906032
360532 cg25152909 0.4300346 0.2746166 0.5854525 6.076684 5.464792 2.0e-07 0.0043413 6.270370 0.0694607 0.0792235 chr5 172566090 C5orf41 172566090
364427 cg25466588 -0.0942618 -0.1322555 -0.0562681 -5.901716 -4.899910 2.3e-06 0.0330400 4.115528 0.9235979 0.0186738 chr3 23958904 NKIRAS1;RPL15 23958904

DMRs

chr start end p length fdr sidak nprobe
1 161008461 161008977 0.00e+00 516 0.00e+00 0.0000000 8
19 21657528 21658001 0.00e+00 473 0.00e+00 0.0000000 5
19 10736005 10736117 0.00e+00 112 0.00e+00 0.0000053 5
20 5485244 5485511 0.00e+00 267 0.00e+00 0.0000034 6
4 79971176 79971432 0.00e+00 256 0.00e+00 0.0000077 4
20 35169593 35169886 0.00e+00 293 0.00e+00 0.0000076 5
1 9099280 9099462 1.00e-07 182 1.00e-07 0.0001413 3
6 26018002 26018185 1.00e-07 183 2.00e-07 0.0002188 6
3 39543966 39544192 2.90e-06 226 3.80e-06 0.0050183 2
15 91473090 91473365 6.10e-06 275 7.40e-06 0.0087499 4
19 12444612 12444741 9.80e-06 129 1.06e-05 0.0293841 5
6 37616597 37616686 8.58e-05 89 8.58e-05 0.3164878 2

Pb

DMP_Pb = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Pb_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb')

# # Unadjusted, N =  333 
# Unadjusted, p<0.05:  13157 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  19418 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.040491 
 
# Number of DMRs identified:   8 

# rm(DMP_Pb); gc()

DMRs

chr start end p length fdr sidak nprobe
10 135051021 135051581 0.0000000 560 0.0000000 0.0000000 11
22 45704901 45705265 0.0000000 364 0.0000000 0.0000000 7
22 19746155 19746368 0.0000000 213 0.0000000 0.0000309 3
3 130745441 130745685 0.0000000 244 0.0000001 0.0000426 10
7 155283139 155283424 0.0000001 285 0.0000001 0.0001025 3
14 104690039 104690244 0.0000001 205 0.0000001 0.0001464 5
6 2891972 2892152 0.0000001 180 0.0000001 0.0001715 5
1 68512776 68512845 0.0001164 69 0.0001164 0.4859412 3
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb/Pb_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb/Pb_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb/Pb_log2_manhattan_DMP_adj.png")

Pb, female

DMP_Pb_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Pb_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_F')

# Unadjusted, N =  158 
# Unadjusted, p<0.05:  10571 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  12301 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.7551375 
 
# Number of identified DMR:  0

# rm(DMP_Pb_F); gc()
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_F/Pb_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_F/Pb_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_F/Pb_log2_manhattan_DMP_adj.png")

Pb, male

DMP_Pb_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Pb_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_M')

# Unadjusted, N =  175 
# Unadjusted, p<0.05:  18362 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  175 
# Adjusted, p<0.05:  12960 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.8922977 
 
# Number of DMRs identified:   5 

# rm(DMP_Pb_M); gc()

DMRs

chr start end p length fdr sidak nprobe
6 33084548 33084985 0.0000000 437 0.0000000 0.0000000 12
1 68512649 68513063 0.0000000 414 0.0000000 0.0000001 7
6 31148331 31148748 0.0000000 417 0.0000000 0.0000008 14
22 45704987 45705265 0.0000001 278 0.0000001 0.0000883 5
19 55973098 55973234 0.0002395 136 0.0002395 0.5007541 3
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_M/Pb_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_M/Pb_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_M/Pb_log2_manhattan_DMP_adj.png")

Se

DMP_Se = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Se_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se')

# Unadjusted, N =  333 
# Unadjusted, p<0.05:  17270 
# Unadjusted, FDR<0.05:  1 
# Unadjusted, pBonf<0.05:  1 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  20323 
# Adjusted, FDR<0.05:  4 
# Adjusted, pBonf<0.05:  1 
# Adjusted, lambda:  0.973855 
 
# Number of DMRs identified:   3 

# rm(DMP_Se); gc()

FDR-significant DMPs

cpg logFC CI.L CI.R AveExpr t P.Value adj.P.Val B adj.P.Val.bonf std_err chr pos gene end
138326 cg08760128 0.2026753 0.1259450 0.2794056 6.725058 5.196935 4e-07 0.0449466 4.356067 0.1436282 0.0387600 chr16 4723507 MGRN1;MGRN1;MGRN1;MGRN1 4723507
157990 cg10145926 0.5456661 0.3464279 0.7449044 5.306680 5.388525 1e-07 0.0274488 5.040732 0.0548975 0.1015708 chr14 95875792 C14orf139 95875792
202444 cg13434714 -0.4219050 -0.5657148 -0.2780953 -5.770270 -5.772209 0e+00 0.0073738 6.470917 0.0073738 0.0732155 chr12 6936787 LEPREL2 6936787
381104 cg26708724 0.5887632 0.3639014 0.8136251 6.732563 5.151581 5e-07 0.0449466 4.196202 0.1797863 0.1146694 chr4 187509785 FAT1 187509785

DMRs

chr start end p length fdr sidak nprobe
17 47091977 47092178 0 201 0 3.70e-06 4
19 50194119 50194252 0 133 0 1.48e-05 5
6 49681177 49681391 0 214 0 2.69e-05 7
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se/Se_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se/Se_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se/Se_log2_manhattan_DMP_adj.png")

Se, female

DMP_Se_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Se_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_F')

# Unadjusted, N =  158 
# Unadjusted, p<0.05:  26254 
# Unadjusted, FDR<0.05:  9 
# Unadjusted, pBonf<0.05:  2 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  16021 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.9294051 
 
# Number of DMRs identified:   3 

# rm(DMP_Se_F); gc()

DMRs

chr start end p length fdr sidak nprobe
6 49681177 49681391 0 214 0 7.00e-07 7
10 38146245 38146671 0 426 0 5.00e-07 9
10 38299241 38299574 0 333 0 1.76e-05 9
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_F/Se_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_F/Se_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_F/Se_log2_manhattan_DMP_adj.png")

Se, male

DMP_Se_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Se_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_M')

# Unadjusted, N =  175 
# Unadjusted, p<0.05:  15593 
# Unadjusted, FDR<0.05:  42 
# Unadjusted, pBonf<0.05:  12 
 
# Adjusted, N =  175 
# Adjusted, p<0.05:  14283 
# Adjusted, FDR<0.05:  28 
# Adjusted, pBonf<0.05:  7 
# Adjusted, lambda:  0.8126609 
 
# Number of DMRs identified:   3 

# rm(DMP_Se_M); gc()

FDR-significant DMPs

cpg logFC CI.L CI.R AveExpr t P.Value adj.P.Val B adj.P.Val.bonf std_err chr pos gene end
15593 cg00908120 0.5923048 0.3575326 0.8270770 6.2892750 4.982761 1.6e-06 0.0400205 1.992248 0.6403278 0.1194751 chr16 72872925 ZFHX3;ZFHX3 72872925
17338 cg01007589 0.7711724 0.4682737 1.0740712 4.7896683 5.028349 1.3e-06 0.0363003 2.109738 0.5219828 0.1543716 chr19 49894178 CCDC155 49894178
26849 cg01588060 -0.2710911 -0.3758947 -0.1662874 -5.9018630 -5.108606 9.0e-07 0.0301990 2.319787 0.3623878 0.0524668 chr6 2245749 GMDS;GMDS 2245749
76780 cg04692924 -0.5882409 -0.7990174 -0.3774643 -6.5844679 -5.511938 1.0e-07 0.0077706 3.394618 0.0555090 0.1071685 chr1 161720042 DUSP12 161720042
82479 cg05051957 -0.6574367 -0.8740830 -0.4407904 -5.6069817 -5.993411 0.0e+00 0.0013886 4.736594 0.0052603 0.1101799 chr8 141522459 CHRAC1;CHRAC1 141522459
107200 cg06723863 -0.3421497 -0.4652900 -0.2190094 -5.9860381 -5.487563 2.0e-07 0.0077706 3.330366 0.0621651 0.0620145 chr16 68270129 ESRP2;ESRP2 68270129
121260 cg07599133 -0.3416695 -0.4778828 -0.2054563 -5.9551590 -4.953937 1.8e-06 0.0427492 1.919754 0.7267357 0.0687928 chr19 35068628 LOC643719 35068628
178008 cg11608893 0.8339746 0.5460968 1.1218524 6.0805801 5.721582 1.0e-07 0.0040380 3.971861 0.0201898 0.1466815 chr6 32059542 TNXB 32059542
186947 cg12243007 0.4392467 0.2665983 0.6118950 -0.7662192 5.024766 1.3e-06 0.0363003 2.100794 0.5302302 0.0875896 chr17 184018 RPH3AL 184018
195368 cg12897502 -0.8409766 -1.1581637 -0.5237896 6.1025868 -5.236485 5.0e-07 0.0183820 2.654338 0.2022023 0.1616851 chr8 67425316 C8orf46 67425316
202444 cg13434714 -0.6278713 -0.8074616 -0.4482811 -5.7834106 -6.904931 0.0e+00 0.0000225 7.412530 0.0000450 0.0911537 chr12 6936787 LEPREL2 6936787
250632 cg16656826 0.2945037 0.1786042 0.4104032 0.1436170 5.018486 1.4e-06 0.0363003 2.085783 0.5445052 0.0582509 chr5 159343871 ADRA1B;ADRA1B 159343871
273355 cg18377660 0.7105200 0.4530993 0.9679406 5.6482645 5.451354 2.0e-07 0.0082254 3.229974 0.0740287 0.1310822 chr1 57535755 DAB1 57535755
281545 cg19005275 0.5865429 0.3677768 0.8053089 4.2897154 5.295308 4.0e-07 0.0153969 2.810608 0.1539686 0.1112673 chr12 113588263 CCDC42B 113588263
311691 cg21373263 0.8225623 0.5510102 1.0941144 3.2926911 5.982561 0.0e+00 0.0013886 4.705737 0.0055543 0.1383211 chr10 126751982 CTBP2;CTBP2 126751982
359398 cg25067702 -0.6449717 -0.8730675 -0.4168760 -6.4012877 -5.584637 1.0e-07 0.0065319 3.593491 0.0391915 0.1160520 chr17 70723227 SLC39A11;SLC39A11 70723227
381104 cg26708724 1.0174549 0.7331142 1.3017956 6.7173655 7.067202 0.0e+00 0.0000186 7.903550 0.0000186 0.1448704 chr4 187509785 FAT1 187509785

DMRs

chr start end p length fdr sidak nprobe
17 70723226 70723386 0.0000000 160 0.0000000 0.0000001 2
4 24796918 24797176 0.0000000 258 0.0000000 0.0000212 6
10 121578383 121578639 0.0000001 256 0.0000001 0.0001182 3
6 30039141 30039175 0.0047996 34 0.0047996 1.0000000 3
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_M/Se_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_M/Se_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_M/Se_log2_manhattan_DMP_adj.png")

Zn

DMP_Zn = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Zn_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn')

# Unadjusted, N =  333 
# Unadjusted, p<0.05:  12854 
# Unadjusted, FDR<0.05:  1 
# Unadjusted, pBonf<0.05:  1 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  23377 
# Adjusted, FDR<0.05:  13 
# Adjusted, pBonf<0.05:  3 
# Adjusted, lambda:  1.10425 

# Number of DMRs identified:   13 

# rm(DMP_Zn); gc()

FDR-significant DMPs

cpg logFC CI.L CI.R AveExpr t P.Value adj.P.Val B adj.P.Val.bonf std_err chr pos gene end
1551 cg00082497 -0.2789683 -0.3788872 -0.1790494 -5.316840 -5.493142 1.0e-07 0.0116179 5.179846 0.0320645 0.0506389 chr1 32802133 MARCKSL1 32802133
15593 cg00908120 0.4887949 0.3055657 0.6720241 6.259296 5.248649 3.0e-07 0.0171923 4.318434 0.1111402 0.0933516 chr16 72872925 ZFHX3;ZFHX3 72872925
66105 cg04015129 0.6544048 0.3991261 0.9096834 4.283036 5.043681 8.0e-07 0.0293642 3.620884 0.3043451 0.1301901 chr10 1058036 GTPBP4 1058036
90290 cg05573434 0.4125276 0.2574161 0.5676391 -3.154237 5.232686 3.0e-07 0.0171923 4.263312 0.1203459 0.0789613 chr4 7648540 SORCS2 7648540
107200 cg06723863 -0.2528131 -0.3544065 -0.1512197 -5.982133 -4.896069 1.6e-06 0.0473985 3.132897 0.6161801 0.0515011 chr16 68270129 ESRP2;ESRP2 68270129
133940 cg08459368 0.5943151 0.3801796 0.8084505 2.645733 5.460643 1.0e-07 0.0116179 5.062990 0.0379479 0.1091583 chr11 61974948 SCGB2A1 61974948
165306 cg10653573 0.8207249 0.5017201 1.1397297 5.432304 5.061929 7.0e-07 0.0293642 3.682080 0.2785931 0.1627524 chr8 141347297 TRAPPC9;TRAPPC9 141347297
202444 cg13434714 -0.4872777 -0.6443364 -0.3302191 -5.770270 -6.104221 0.0e+00 0.0011936 7.460402 0.0011936 0.0799582 chr12 6936787 LEPREL2 6936787
234745 cg15528091 -0.3070787 -0.4271830 -0.1869744 -6.355947 -5.030429 8.0e-07 0.0293642 3.577005 0.3242929 0.0610193 chr19 18119069 ARRDC2;ARRDC2;ARRDC2 18119069
248112 cg16496814 0.2140204 0.1314881 0.2965527 5.206564 5.102050 6.0e-07 0.0286288 3.817765 0.2290303 0.0416708 chr11 9778721 9778721
281636 cg19011752 0.2463497 0.1496666 0.3430328 -2.537801 5.013200 9.0e-07 0.0293642 3.519541 0.3523705 0.0489723 chr21 45772638 TRPM2 45772638
338217 cg23477849 0.2605321 0.1652481 0.3558161 4.877957 5.379658 1.0e-07 0.0116179 4.776453 0.0573879 0.0482514 chr19 5698492 LONP1 5698492
370410 cg25954729 -0.2155491 -0.2944166 -0.1366816 -6.344974 -5.377269 1.0e-07 0.0116179 4.768033 0.0580895 0.0397755 chr11 66610784 RCE1;C11orf80;RCE1 66610784

DMRs

chr start end p length fdr sidak nprobe
12 54070516 54070610 0.0000000 94 0.0000000 0.0000052 5
19 18118799 18119069 0.0000000 270 0.0000000 0.0000098 3
10 124638975 124639260 0.0000000 285 0.0000001 0.0000233 12
20 25129295 25129562 0.0000001 267 0.0000002 0.0001003 8
6 32063990 32064258 0.0000001 268 0.0000002 0.0001031 12
4 7648539 7648627 0.0000001 88 0.0000002 0.0003372 2
8 41655672 41655894 0.0000001 222 0.0000002 0.0002389 4
6 41168800 41169049 0.0000001 249 0.0000002 0.0002207 6
17 1395863 1396123 0.0000002 260 0.0000002 0.0002547 5
17 79503641 79503877 0.0000002 236 0.0000002 0.0002943 4
12 54385274 54385526 0.0000002 252 0.0000002 0.0002909 4
22 45704987 45705042 0.0000002 55 0.0000002 0.0014895 4
20 35169593 35169846 0.0004351 253 0.0004351 0.4926596 3
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn/Zn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn/Zn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn/Zn_log2_manhattan_DMP_adj.png")

Zn, female

DMP_Zn_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Zn_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_F')

# # Unadjusted, N =  158 
# Unadjusted, p<0.05:  12830 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  17143 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.9412223 
 
# Number of DMRs identified:   3 

# rm(DMP_Zn_F); gc()

DMRs

chr start end p length fdr sidak nprobe
11 73357018 73357396 0.0e+00 378 0.0e+00 0.0000000 8
1 120174148 120174361 7.0e-07 213 1.1e-06 0.0013294 2
10 124638975 124639012 1.1e-05 37 1.1e-05 0.1109657 4
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_F/Zn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_F/Zn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_F/Zn_log2_manhattan_DMP_adj.png")

Zn, male

DMP_Zn_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Zn_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_M')

# Unadjusted, N =  175 
# Unadjusted, p<0.05:  16787 
# Unadjusted, FDR<0.05:  36 
# Unadjusted, pBonf<0.05:  8 
 
# Adjusted, N =  175 
# Adjusted, p<0.05:  14737 
# Adjusted, FDR<0.05:  36 
# Adjusted, pBonf<0.05:  3 
# Adjusted, lambda:  0.8766913 
 
# Number of DMRs identified:   16 

# rm(DMP_Zn_M); gc()

FDR-significant DMPs

cpg logFC CI.L CI.R AveExpr t P.Value adj.P.Val B adj.P.Val.bonf std_err chr pos gene end
15593 cg00908120 0.7986746 0.5264258 1.0709234 6.2892750 5.793958 0.0e+00 0.0052948 3.3135597 0.0141641 0.1385227 chr16 72872925 ZFHX3;ZFHX3 72872925
17338 cg01007589 0.9065622 0.5465007 1.2666237 4.7896683 4.972701 1.7e-06 0.0267901 1.3379386 0.6697528 0.1835056 chr19 49894178 CCDC155 49894178
18335 cg01063965 -0.2692683 -0.3808800 -0.1576566 -6.4353826 -4.764741 4.2e-06 0.0451214 0.8668535 1.0000000 0.0555811 chr11 695461 TMEM80;TMEM80;DEAF1;DEAF1 695461
24635 cg01447660 0.4161258 0.2471860 0.5850656 -0.9207246 4.864703 2.7e-06 0.0334209 1.0923878 1.0000000 0.0854122 chr2 69152678 69152678
25935 cg01533258 -0.3013596 -0.4269158 -0.1758034 -6.4562972 -4.740350 4.7e-06 0.0463873 0.8122693 1.0000000 0.0628818 chr14 95235489 GSC 95235489
36678 cg02196294 -0.2906897 -0.4099158 -0.1714636 -5.4126781 -4.815283 3.4e-06 0.0372147 0.9805256 1.0000000 0.0595727 chr6 39197260 KCNK5 39197260
41497 cg02490920 0.3948042 0.2423949 0.5472136 1.3358885 5.116039 9.0e-07 0.0166832 1.6720694 0.3503468 0.0768511 chr3 50304406 SEMA3B;SEMA3B 50304406
45187 cg02711608 0.5447487 0.3462840 0.7432134 -2.0855657 5.421025 2.0e-07 0.0122834 2.3968616 0.0853542 0.1006441 chr19 47287964 SLC1A5;SLC1A5;SLC1A5;SLC1A5 47287964
49479 cg02968175 0.3308394 0.2054185 0.4562602 5.7555141 5.209681 6.0e-07 0.0127085 1.8924369 0.2282507 0.0628111 chr16 4690020 MGRN1;MGRN1;MGRN1;MGRN1 4690020
55565 cg03352332 0.8979978 0.5628181 1.2331775 5.5379777 5.291381 4.0e-07 0.0123746 2.0848241 0.1568056 0.1707666 chr3 186360953 FETUB 186360953
66105 cg04015129 0.8663699 0.5510958 1.1816440 4.2710633 5.427334 2.0e-07 0.0122834 2.4113963 0.0829347 0.1605719 chr10 1058036 GTPBP4 1058036
71895 cg04374006 0.2627697 0.1559793 0.3695602 -0.2704598 4.859668 2.8e-06 0.0334209 1.0809686 1.0000000 0.0530461 chr19 33556395 RHPN2 33556395
72385 cg04406071 -0.3235390 -0.4464810 -0.2005970 -6.0707229 -5.197446 6.0e-07 0.0127085 1.8635148 0.2414621 0.0615161 chr17 59489784 C17orf82 59489784
76780 cg04692924 -0.6620566 -0.9146336 -0.4094796 -6.5844679 -5.176935 7.0e-07 0.0132956 1.8135106 0.2659111 0.1284330 chr1 161720042 DUSP12 161720042
82479 cg05051957 -0.6556186 -0.9211778 -0.3900594 -5.6069817 -4.875974 2.6e-06 0.0334209 1.1167256 1.0000000 0.1350923 chr8 141522459 CHRAC1;CHRAC1 141522459
107200 cg06723863 -0.3660155 -0.5147452 -0.2172859 -5.9860381 -4.860330 2.8e-06 0.0334209 1.0824690 1.0000000 0.0749420 chr16 68270129 ESRP2;ESRP2 68270129
117957 cg07380021 -0.6557600 -0.9015723 -0.4099477 -5.4253082 -5.268813 4.0e-07 0.0124371 2.0310571 0.1741199 0.1249619 chr1 206755252 RASSF5;RASSF5;RASSF5 206755252
138326 cg08760128 0.3591892 0.2311150 0.4872635 6.7313293 5.538922 1.0e-07 0.0121638 2.6848170 0.0486553 0.0641960 chr16 4723507 MGRN1;MGRN1;MGRN1;MGRN1 4723507
143452 cg09127400 -0.3253080 -0.4612252 -0.1893909 -5.8091855 -4.726984 5.0e-06 0.0479454 0.7824329 1.0000000 0.0682830 chr6 30712331 IER3 30712331
159790 cg10266648 1.0393561 0.6292003 1.4495119 5.9758418 5.004802 1.5e-06 0.0241741 1.4119349 0.5801792 0.2091418 chr2 106560529 106560529
165306 cg10653573 1.4145550 0.8990686 1.9300414 5.3698793 5.419686 2.0e-07 0.0122834 2.3929054 0.0859836 0.2630143 chr8 141347297 TRAPPC9;TRAPPC9 141347297
168880 cg10923018 0.3112659 0.1850396 0.4374922 2.7253233 4.870183 2.7e-06 0.0334209 1.1048470 1.0000000 0.0632316 chr6 31743769 C6orf27 31743769
180170 cg11761483 -0.7173589 -0.9874920 -0.4472257 -5.5960630 -5.244814 5.0e-07 0.0127085 1.9740228 0.1945730 0.1374378 chr17 70723386 SLC39A11;SLC39A11 70723386
202444 cg13434714 -0.8386175 -1.0430621 -0.6341729 -5.7834106 -8.101361 0.0e+00 0.0000001 9.4776845 0.0000001 0.1037179 chr12 6936787 LEPREL2 6936787
216196 cg14230280 1.2229340 0.7320030 1.7138651 4.2784975 4.919874 2.1e-06 0.0313748 1.2167946 0.8471192 0.2504580 chr9 132502800 PTGES 132502800
248112 cg16496814 0.3215835 0.2022500 0.4409170 5.2206210 5.322247 3.0e-07 0.0123746 2.1603427 0.1354705 0.0596289 chr11 9778721 9778721
250632 cg16656826 0.3445219 0.2066488 0.4823949 0.1436170 4.935159 2.0e-06 0.0303861 1.2531114 0.7900373 0.0693009 chr5 159343871 ADRA1B;ADRA1B 159343871
257216 cg17155018 -1.0196926 -1.4432541 -0.5961312 1.3941337 -4.754713 4.4e-06 0.0455985 0.8432207 1.0000000 0.2160003 chr6 111953066 111953066
268589 cg18037826 0.4119927 0.2555297 0.5684556 4.2937576 5.200460 6.0e-07 0.0127085 1.8706351 0.2381405 0.0789525 chr12 109273835 DAO 109273835
281545 cg19005275 0.7482069 0.4921296 1.0042842 4.2897154 5.770615 0.0e+00 0.0052948 3.2552389 0.0158843 0.1302288 chr12 113588263 CCDC42B 113588263
286872 cg19439837 0.9459971 0.5527040 1.3392901 6.9655374 4.750562 4.5e-06 0.0455985 0.8339344 1.0000000 0.2005136 chr12 4923529 KCNA6;KCNA6 4923529
288096 cg19532212 0.7606680 0.4803455 1.0409904 4.4209486 5.359308 3.0e-07 0.0123746 2.2474246 0.1142103 0.1426619 chr17 56769430 TEX14;RAD51C;TEX14;RAD51C 56769430
311691 cg21373263 0.8805707 0.5515533 1.2095881 3.2926911 5.285874 4.0e-07 0.0123746 2.0716919 0.1608692 0.1676110 chr10 126751982 CTBP2;CTBP2 126751982
322216 cg22240394 1.2229725 0.7670216 1.6789234 6.8239404 5.297489 4.0e-07 0.0123746 2.0993979 0.1524156 0.2325683 chr3 186211630 186211630
324251 cg22413938 -0.3880547 -0.5460152 -0.2300942 -4.5630336 -4.851858 2.9e-06 0.0335705 1.0632521 1.0000000 0.0797285 chr14 78447481 78447481
338217 cg23477849 0.3810081 0.2311925 0.5308237 4.8962493 5.022741 1.4e-06 0.0232259 1.4548453 0.5341954 0.0755056 chr19 5698492 LONP1 5698492
339781 cg23601521 0.7996758 0.4972086 1.1021431 4.8708259 5.221641 5.0e-07 0.0127085 1.9190935 0.2165310 0.1540110 chr2 50275179 NRXN1;NRXN1;NRXN1 50275179
370410 cg25954729 -0.3034838 -0.4163024 -0.1906653 -6.3724574 -5.312742 4.0e-07 0.0123746 2.1375974 0.1416105 0.0562146 chr11 66610784 RCE1;C11orf80;RCE1 66610784
379632 cg26608798 0.3969674 0.2358372 0.5580975 0.5750420 4.865660 2.7e-06 0.0334209 1.0945703 1.0000000 0.0813703 chr16 33853544 33853544
381104 cg26708724 0.9252394 0.5664932 1.2839856 6.7173655 5.093758 1.0e-06 0.0176594 1.6184667 0.3885072 0.1828323 chr4 187509785 FAT1 187509785
392164 cg27503275 0.4776627 0.2828083 0.6725171 4.1214740 4.841489 3.0e-06 0.0341627 1.0390945 1.0000000 0.0987864 chr6 3880016 3880016

DMRs

chr start end p length fdr sidak nprobe
17 70723226 70723386 0.0000000 160 0.0000000 0.0000026 2
10 121578136 121578639 0.0000000 503 0.0000000 0.0000012 4
14 78447480 78447640 0.0000000 160 0.0000000 0.0000126 3
19 50194119 50194252 0.0000000 133 0.0000000 0.0000160 5
4 186732836 186733060 0.0000000 224 0.0000000 0.0000130 7
4 24796918 24797176 0.0000000 258 0.0000000 0.0000182 6
14 76734326 76734605 0.0000000 279 0.0000000 0.0000220 5
21 45773781 45773997 0.0000000 216 0.0000000 0.0000374 2
5 135416204 135416613 0.0000000 409 0.0000000 0.0000256 9
11 63679431 63679637 0.0000001 206 0.0000001 0.0001231 2
20 62716331 62716606 0.0000001 275 0.0000001 0.0001330 4
17 78549323 78549371 0.0000001 48 0.0000002 0.0011147 3
5 1868136 1868357 0.0000004 221 0.0000005 0.0007368 4
22 45704987 45705042 0.0000015 55 0.0000017 0.0104801 4
5 176755392 176755449 0.0000127 57 0.0000135 0.0839213 2
2 88583556 88583805 0.0001042 249 0.0001042 0.1522101 3
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_M/Zn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_M/Zn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_M/Zn_log2_manhattan_DMP_adj.png")